Long Term Supported Release - October 28th, 2020: JChem PostgreSQl Cartridge 20.19.1 (Gallium.1)
No changes.
New, simpler syntax is available for full fragment search. Documentation
The use of normal canonical tautomers in full fragment search is also available . Documentation
Dropping index is necessary before upgrade in JPC.
jchem-psql service could not be restarted in some cases.
Molecule initialization at import or search for markush structures with a lot of enumerants was not stopped in the JChem Server when the query was cancelled.
Consideration of chiral flag can be set by stereoAssumption=RELATIVE parameter in molecule type definition files. Documentation
New tautomerization method added to the molecule type definitions called CANONIC_GENERIC_HYBRID. Documentation
Non-valid structures can be imported and indexed. However, they won't hit any structure, including themselves.
JPC is put to frequent release its version equals other projects'. Documentation is not bundled.
AIOBE could have been thrown in case of some standardizer configuration.
Large structures with stereo configuration could be incorrectly handled.
Non-polymer query was not found in polymer targets if it was matching on end groups.
Tautomer duplicate search didn't find hits for some structures with tetrahedral stereo information.
JPC can run in highly available mode. Documentation
Searching with ignored tetrahedral stereo information has been introduced. Documentation
The speed of stereo search has been increased by approximately 90%.
Unlogged index creation failed.
Tautomer search could give false hits with queries containing explicit Hydrogen atoms.
Tautomerization of structures with valence error could be erroneous.
PostgreSQL 12 is the only supported PostgeSQL version from now on.
Monitoring of index creation progress is enabled. Documentation
Cache size decreased by 20% for target-type datasets.
15% indexing speed improvement.
20-50% search speedup for frequent queries
Vacuum speed up for large tables.
Cost estimation has been improved, joined queries run faster.
Nitrogen in marked stereo configuration matched unmarked chiral center.
Small ring cis double bond stereo configurations were recognized as trans in case of trans perspective drawing in 3D.
JChem Service can be installed on other instance than the PostgreSQL database.
Pseudo formula handling has been added to chemical terms .
Allow NULL values in queries and molecular columns of tables.
Standardize method added.
No changes.
Chemical term evaluation could cause OperationAbortedException because of concurrency problems.
Initializing jchem-psql service sometimes failed because of missing log folder.
Default fingerprint size is reduced from 1024 to 512.
Upgrade of Thrift to 0.11.0.
Copy of binary data was erroneous.
Chemical terms returning a list of values (e.g. logD) did not return the values.
Polymers with ambiguous aromatic rings in end groups could not be indexed.
PostgreSQL 10 is supported from now on.
Parallel sequential scan mode is supported.
Indexing speed has been increased.
Log4j logging is implemented. Documentation
New cache parameters are provided for performance tuning of searches. Documentation
Peptide sequence file format was not handled correctly in the searches. From now on the 3-letter peptide format works in searches.
Duplicate search could be slow when the target structure contained charged hydrogen atom.
Similarity search did not always return hits in the order of similarity.
Molfiles with sgroups embedded in SRU groups were not handled.
Missing hits could have been experienced in tautomer duplicate search in case of InChi files.
jchem-psql service could crash if erroneous query structure was applied in a query.
Service jchem-psql stop did not work on some new Ubuntu versions.
Known issue present in version 2.8 has been solved.
Similarity search did not always return hits in the order of similarity.
Molfiles with sgroups embedded in SRU groups were not handled.
Missing hits could have been experienced in tautomer duplicate search in case of InChi files.
jchem-psql service could crash if erroneous query structure was applied in a query.
Service jchem-psql stop did not work on some new Ubuntu versions.
/var/lib/jchem-psql/store/ have been hugely increased.Molecules with small rings containing double bonds could miss duplicates when duplicate search was performed.
Tautomer duplicate search could result false negative hits.
Index creation threw exception in case of molecules having deuterium atom.
Tautomer duplicate search could result false positive hits.
Reaction search is supported from now on. Documentation
Searching structures containing rings is sped-up.
Duplicate search could result failing hits in tables indexed with chemindex.
Misleading warning: WARNING: molecule_ops.cpp:205 Cost estimation values were not calculated has been fixed.
Searches with joined queries and with limit <n> conditions has been improved due to cost estimation and function mode search enhancements.
Limitation of the number of jchem-psql service sessions is configurable by the administrator. Documentation
Searches combining more than three SELECT statements with logical operators could run into dead lock state.
Relevance calculation threw exception in case of polymer and query structures.
Relevance calculation could throw license exception even if the postgresql license was present.
Custom standardizer.xml applied in type definition generated exception when more than one molecules were inserted in one statement.
Relevance sorting possibility of the search hits is provided. Documentation
Collecting invalid molecules during sdf import and (cx)smiles/(cx)smarts import is available.
New function, is_valid_molecule, is introduced.
Memory size requirement of searches in big tables has been decreased, and further performance tuning possibilities are provided. Documentation
Tautomer substructure search could result false negative hits in case of aromatic structures.
Index entries were overridden by each other in some cases resulting loss of hits.
The use of chemical terms is implemented. Documentation
The performance of searching with combined queries can be tuned by calibration. Documentation